The paper presents the proposal of a leakage prediction method in flange joints, after pipeline deformation, based on FEM (Finite Element Methods). The stages of developing the design are discussed, and a complex, multi-stage method of applying the loads is presented in detail. Moreover, the gasket material data obtained in experiments were used. The paper also presents the results of calculations on a non-uniform stress distribution in the radial direction of the gasket. In addition, it has been shown that the deflection of the pipeline with a minor displacement causes an increase in the diversification of the circumferential pressure of the gasket, and also has a significant influence on the determination of the actual state of stress to which the gasket is subject. Moreover, it was found that the distribution of contact pressure on the deflection of the pipeline has a significant influence on the level of leakage. The results of tests are compared to the results of the numerical calculations of the stress in bolts. By comparing the bolt tension changes obtained by numerical and experiment analyses, it has been shown that the assumptions made in developing the numerical model are correct.